BACKGROUND In rare cases, odontogenic keratocysts (ODs) transform into squamous cell carcinoma. Intervals between the first attendance of a patient and the diagnosis of OD with malignant transformation vary from weeks to years. In this article, we report a case of malignancy derived from OD with a five-day delay in diagnosis. CASE SUMMARY A 54-year-old woman was referred to Tongji Hospital in Wuhan, China with complaints of moderate pain, recurrent swelling, and pus discharge around her left maxillary lateral incisor for over 10 years. Physical examination revealed a fistula at the palatine-side mucoperiosteum of the left maxillary lateral incisor and enlarged lymph node in the left neck. Cone beam computed tomography revealed a cystic lesion with massive bone destruction from the left maxillary central incisor to the left secondary maxillary premolar and local bony destruction in the left first mandibular molar. The patient was clinically diagnosed with OD. Enucleation rather than marsupialization was performed given the risk factors of long history, recent aggravated pain, and massive bony destruction. Malignant transformation of OD was confirmed by pathologists 3 d after the operation. Radical surgery was performed, and lymph node metastasis was observed. The patient was subjected to postoperative radiotherapy and synchronous chemotherapy, and no local recurrence or distant metastasis was noted at one-year follow-up. CONCLUSION Our case suggests that clinicians should be aware of the malignant transformation of OD, especially when patients present with a long history, massive cyst, chronic inflammation, recent persistent infections, aggravated pain, numbness around the cystic lesion, and lymph node enlargement.